Vectors based on adeno-associated virus (AAV) are believed to have utility for gene therapy but a significant obstacle has been the difficulty in generating such vectors in amounts that would be clinically useful for human gene therapy applications. This is a particular problem for in vivo applications such as direct delivery to the lung. Another important goal in the gene therapy context, discussed in more detail herein, is the production of vector preparations that are essentially free of replication-competent virions. The following description briefly summarizes studies involving adeno-associated virus and AAV vectors, and then describes a number of novel improvements according to the present invention that are useful for efficiently generating high titer recombinant AAV vector (rAAV) preparations suitable for use in gene therapy.
Adeno-associated virus is a defective parvovirus that grows only in cells in which certain functions are provided by a co-infecting helper virus. General reviews of AAV may be found in, for example, Carter, 1989, Handbook of Parvoviruses, Vol. I, pp. 169-228, and Berns, 1990, Virology, pp. 1743-1764, Raven Press, (New York). Examples of co-infecting viruses that provide helper functions for AAV growth and replication are adenoviruses, herpesviruses and, in some cases, poxviruses such as vaccinia. The nature of the helper function is not entirely known but it appears that the helper virus indirectly renders the cell permissive for AAV replication. This belief is supported by the observation that AAV replication may occur at low efficiency in the absence of helper virus co-infection if the cells are treated with agents that are either genotoxic or that disrupt the cell cycle.
Although AAV may replicate to a limited extent in the absence of helper virus, under such conditions as noted above, more generally infection of cells with AAV in the absence of helper functions results in the proviral AAV genome integrating into the host cell genome. Unlike other viruses, such as many retroviruses, it appears that AAV generally integrates into a unique position in the human genome. Thus, it has been reported that, in human cells, AAV integrates into a unique position (referred to as an “AAV integration site”) which is located on chromosome 19. See, e.g., Weitzman et al. (1994) Proc. Natl. Acad. Sci. USA 91: 5808-5812. If host cells having an integrated AAV are subsequently superinfected with a helper virus such as adenovirus, the integrated AAV genome can be rescued and replicated to yield a burst of infectious progeny AAV particles. A sequence at the AAV integration site, referred to as “P1”, shares limited homology with the AAV inverted terminal repeat (ITR) sequence, exhibits Rep binding activity in a cell-free replication system, and is believed to be involved in both the integration and rescue of AAV. See, e.g., Weitzman et al., id., Kotin et al. (1992) EMBO J. 11:5071-5078, and Urcelay et al., J. Virol. 69: 2038-2046. The fact that integration of AAV appears to be efficient and site-specific makes AAV a useful vector for introducing genes into cells for uses such as human gene therapy.
AAV has a very broad host range without any obvious species or tissue specificity and can replicate in virtually any cell line of human, simian or rodent origin provided that an appropriate helper is present. AAV is also relatively ubiquitous and has been isolated from a wide variety of animal species including most mammalian and several avian species.
AAV is not associated with the cause of any disease. Nor is AAV a transforming or oncogenic virus, and integration of AAV into the genetic material of human cells generally does not cause significant alteration of the growth properties or morphological characteristics of the host cells. These properties of AAV also recommend it as a potentially useful human gene therapy vector because most of the other viral systems proposed for this application, such as retroviruses, adenoviruses, herpesviruses, or poxviruses, are disease-causing.
Although various serotypes of AAV are known to exist, they are all closely related functionally, structurally, and at the genetic level (see, e.g., Blacklow, 1988, pp. 165-174 of Parvoviruses and Human Disease, J. R. Pattison (ed.); and Rose, 1974, Comprehensive Virology 3: 1-61). For example, all AAV serotypes apparently exhibit very similar replication properties mediated by homologous rep genes; and all bear three related capsid proteins such as those expressed in AAV2. The degree of relatedness is further suggested by heteroduplex analysis which reveals extensive cross-hybridization between serotypes along the length of the genome; and the presence of analogous self-annealing segments at the termini that correspond to inverted terminal repeats (ITRs). The similar infectivity patterns also suggest that the replication functions in each serotype are under similar regulatory control. Thus, although the AAV2 serotype was used in various illustrations of the present invention that are set forth in the Examples, general reference to AAV herein encompasses all AAV serotypes, and it is fully expected that the methods and compositions disclosed herein will be applicable to all AAV serotypes.
AAV particles comprise a proteinaceous capsid having three capsid proteins, VP1, VP2 and VP3, which enclose a DNA genome. The AAV2 DNA genome, for example, is a linear single-stranded DNA molecule having a molecular weight of about 1.5×106 daltons and a length of about 5 kb. Individual particles package only one DNA molecule strand, but this may be either the “plus” or “minus” strand. Particles containing either strand are infectious and replication occurs by conversion of the parental infecting single strand to a duplex form and subsequent amplification of a large pool of duplex molecules from which progeny single strands are displaced and packaged into capsids. Duplex or single-strand copies of AAV genomes can be inserted into bacterial plasmids or phagemids and transfected into adenovirus-infected cells; these techniques have facilitated the study of AAV genetics and the development of AAV vectors.
The AAV genome, which encodes proteins mediating replication and encapsidation of the viral DNA, is generally flanked by two copies of inverted terminal repeats (ITRs). In the case of AAV2, for example, the ITRs are each 145 nucleotides in length, flanking a unique sequence region of about 4470 nucleotides that contains two main open reading frames for the rep and cap genes (Srivastiva et al., 1983, J. Virol., 45:555-564; Hermonat et al., 1984, J. Virol. 51:329-339; Tratschin et al., 1984, J. Virol., 51:611-619). The AAV2 unique region contains three transcription promoters p5, p19, and p40 (Laughlin et al., 1979, Proc. Natl. Acad. Sci. USA, 76:5567-5571) that are used to express the rep and cap genes. The ITR sequences are required in cis and are sufficient to provide a functional origin of replication (ori), signals required for integration into the cell genome, and efficient excision and rescue from host cell chromosomes or recombinant plasmids. It has also been shown that the ITR can function directly as a transcription promoter in an AAV vector. See Carter et al., U.S. Pat. No. 5,587,308.
The rep and cap gene products are required in trans to provide functions for replication and encapsidation of viral genome, respectively. Again, using AAV2 for purposes of illustration, the rep gene is expressed from two promoters, p5 and p19, and produces four proteins. Transcription from p5 yields an unspliced 4.2 kb mRNA encoding a first Rep protein (Rep78), and a spliced 3.9 kb mRNA encoding a second Rep protein (Rep68). Transcription from p19 yields an unspliced mRNA encoding a third Rep protein (Rep52), and a spliced 3.3 kb mRNA encoding a fourth Rep protein (Rep40). Thus, the four Rep proteins all comprise a common internal region sequence but differ in their amino and carboxyl terminal regions. Only the large Rep proteins (i.e. Rep78 and Rep68) are required for AAV duplex DNA replication, but the small Rep proteins (i.e. Rep52 and Rep40) appear to be needed for progeny, single-strand DNA accumulation (Chejanovsky & Carter, 1989, Virology 173:120-128). Rep68 and Rep78 bind specifically to the hairpin conformation of the AAV ITR and possess several enzyme activities required for resolving replication at the AAV termini. Rep52 and Rep40 have none of these properties. Reports by C. Hölscher et al. (1994, J. Virol. 68:7169-7177; and 1995, J. Virol. 69:6880-6885) have suggested that expression of Rep78 or Rep 68 may in some circumstances be sufficient for infectious particle formation.
The Rep proteins, primarily Rep78 and Rep68, also exhibit pleiotropic regulatory activities including positive and negative regulation of AAV genes and expression from some heterologous promoters, as well as inhibitory effects on cell growth (Tratschin et al., 1986, Mol. Cell. Biol. 6:2884-2894; Labow et al., 1987, Mol. Cell. Biol., 7:1320-1325; Khleifet al., 1991, Virology, 181:738-741). The AAV p5 promoter is negatively auto-regulated by Rep78 or Rep68 (Tratschin et al., 1986). Due to the inhibitory effects of expression of rep on cell growth, constitutive expression of rep in cell lines has not been readily achieved. For example, Mendelson et al. (1988, Virology, 166:154-165) reported very low expression of some Rep proteins in certain cell lines after stable integration of AAV genomes.
The capsid proteins VP1, VP2, and VP3 share a common overlapping sequence, but VP1 and VP2 contain additional amino terminal sequences. All three proteins are encoded by the same cap gene reading frame typically expressed from a spliced 2.3 kb mRNA transcribed from the p40 promoter. VP2 and VP3 can be generated from this mRNA by use of alternate initiation codons. Generally, transcription from p40 yields a 2.6 kb precursor mRNA which can be spliced at alternative sites to yield two different transcripts of about 2.3 kb. VP2 and VP3 can be encoded by either transcript (using either of the two initiation sites), whereas VP1 is encoded by only one of the transcripts. VP3 is the major capsid protein, typically accounting for about 90% of total virion protein. VP1 is coded from a minor mRNA using a 3′ donor site that is 30 nucleotides upstream from the 3′ donor used for the major mRNA that encodes VP2 and VP3. All three proteins are required for effective capsid production. Mutations which eliminate all three proteins (Cap-negative) prevent accumulation of single-strand progeny AAV DNA, whereas mutations in the VP1 amino-terminus (“Lip-negative” or “Inf-negative”) can permit assembly of single-stranded DNA into particles but the infectious titer is greatly reduced.
The genetic analysis of AAV described above was largely based upon mutational analysis of AAV genomes cloned into bacterial plasmids. In early work, molecular clones of infectious genomes of AAV were constructed by insertion of double-strand molecules of AAV into plasmids by procedures such as GC-tailing (Samulski et al., 1982, Proc. Natl. Acad. Sci. USA, 79:2077-2081), addition of synthetic linkers containing restriction endonuclease cleavage sites (Laughlin et al., 1983, Gene, 23:65-73) or by direct, blunt-end ligation (Senapathy & Carter, 1984, J. Biol. Chem., 259:4661-4666). Transfection of such AAV recombinant plasmids into mammalian cells that were also infected with an appropriate helper virus, such as adenovirus, resulted in rescue and excision of the AAV genome free of any plasmid sequence, replication of the rescued genome and generation of progeny infectious AAV particles. This provided the basis for performing genetic analysis of AAV as summarized above and permitted construction of AAV transducing vectors.
There are at least two desirable features of any AAV vector designed for use in human gene therapy. The first is that the transducing vector be generated at titers sufficiently high to be practicable as a delivery system. This is especially important for gene therapy strategies aimed at in vivo delivery of the vector. For example, it is likely that for many desirable applications of AAV vectors, such as treatment of cystic fibrosis by direct in vivo delivery to the airway, the desired dose of transducing vector may be from 108 to 1010, or, in some cases, in excess of 1010 particles. Secondly, the vector preparations are preferably essentially free of wild-type AAV virus (or any replication-competent AAV). The attainment of high titers of AAV vectors has been difficult for several reasons including preferential encapsidation of wild-type AAV genomes (if they are present or generated by recombination), and the difficulty in generating sufficient complementing functions such as those provided by the wild-type rep and cap genes. Useful cell lines expressing such complementing functions have been especially difficult to generate, in part because of pleiotropic inhibitory functions associated with the rep gene products. Thus, cell lines in which the rep gene is integrated and expressed may grow slowly or express rep at very low levels.
Based on genetic analyses described above, the general principles of AAV vector construction have been described. See, for example, Carter, 1992, Current Opinions in Biotechnology, 3:533-539; Muzyczka, 1992, Curr. Topics in Microbiol. and Immunol., 158:97-129. AAV vectors are generally constructed in AAV recombinant plasmids by substituting portions of the AAV coding sequence with foreign DNA to generate a recombinant AAV (rAAV) vector or “pro-vector”. It is well established in the AAV literature that, in the vector, the terminal (ITR) portions of the AAV sequence must be retained intact because these regions are required in cis for several functions, including excision from the plasmid after transfection, replication of the vector genome and integration and rescue from a host cell genome. In some situations, providing a single ITR may be sufficient to carry out the functions normally associated with two wild-type ITRs (see, e.g., Samulski et al., WO 94/13788, published 23 Jun. 1994).
As described in the art, AAV ITRs generally consist of a palindromic hairpin (HP) structure and a 20-nucleotide region, designated the D-sequence, that is not involved in the HP formation. Wang et al. identified AAV ITR sequences required for rescue, replication and encapsidation of the AAV genome (Wang et al., 1996, J. Virol. 70:1668-1677). Wang et al. (1996) reported the following: (i) two HP structures and one D-sequence are sufficient for efficient rescue and preferential replication of the AAV DNA, (ii) two HP structures alone allow a low level rescue and replication of the AAV DNA, but rescue and replication of the AAV vector DNA sequences also occur in the absence of the of the D-sequences, (iii) one HP structure and two D-sequences, but not one HP structure and one D-sequence, also allow rescue and replication of the AAV as well as the vector DNA sequences, (iv) one HP structure alone or two D-sequences but not one D-sequence alone allows replication of full length plasmid DNA but no rescue of the AAV genome occurs, (v) no rescue-replication occurs in the absence of the HP structures and D-sequence, (vi) in the absence of the D-sequences, the HP structures are insufficient for successsful encapsidation of the AAV genomes, and (vii) the AAV genomes containing only one ITR structure can be packaged into biologically active virions. Thus, Wang et al. conclude that the D-sequence plays a crucial role in the efficient rescue and selective replication and encapsidation of the AAV genome. Subsequent studies published by this group suggested that the first 10 nucleotides of the D-sequence proximal to the hairpin structure of the ITR are necessary and sufficient for optimal rescue and replication of the AAV genome (Wang et al., 1997, J. Virol. 71:3077-3082). Thus, this work identifies the D-sequence as required for packaging of the AAV genome.
The vector can then be packaged into an AAV particle to generate an AAV transducing virus by transfection of the vector into cells that are infected by an appropriate helper virus such as adenovirus or herpesvirus; provided that, in order to achieve replication and encapsidation of the vector genome into AAV particles, the vector must generally be complemented for any AAV functions required in trans, particularly rep and cap, that were deleted in construction of the vector.
Such AAV vectors are among a small number of recombinant virus vector systems which have been shown to have utility as in vivo gene transfer agents (reviewed in Carter, 1992; Muzyczka, 1992) and thus are potentially of great importance for human gene therapy. AAV vectors are capable of high-frequency transduction and expression in a variety of cells including cystic fibrosis (CF) bronchial and nasal epithelial cells (see, e.g., Flotte et al., 1992, Am. J. Respir. Cell Mol. Biol. 7:349-356; Egan et al., 1992, Nature, 358:581-584; Flotte et al., 1993a, J. Biol. Chem. 268:3781-3790; and Flotte et al., 1993b, Proc. Natl. Acad. Sci. USA, 93:10163-10167); human bone marrow-derived erythroleukemia cells (see, e.g., Walsh et al., 1992, Proc. Natl. Acad. Sci. USA, 89:7257-7261); as well as brain, eye and muscle cells. AAV may not require active cell division for transduction and expression which would be another clear advantage over retroviruses, especially in tissues such as the human airway epithelium where most cells are terminally differentiated and non-dividing.
There is a significant need for methods that can be used to efficiently generate recombinant vectors encapsidated in AAV particles that are essentially free of wild-type or other replication-competent AAV; and a corresponding need for cell lines that can be used to effectively generate such recombinant vectors. The present invention provides methods, compositions, and cells for the production of high-titer, AAV particle-encapsidated, recombinant vector preparations.
All publications and patent applications cited herein are hereby incorporated by reference in their entirety.